X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=d4c6009acdd70d964de8b8d5d5546d3139374c70;hb=933794f42ed55d57850424e3459a54cd2d92c933;hp=0df1585dc6430dbdd62c7f704f3f2404dde96a1c;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index 0df1585..d4c6009 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -21,8 +21,12 @@ package jalview.gui; import jalview.analysis.AlignmentSorter; +import jalview.analysis.AverageDistanceTree; import jalview.analysis.NJTree; +import jalview.analysis.TreeBuilder; +import jalview.analysis.TreeModel; import jalview.api.analysis.ScoreModelI; +import jalview.api.analysis.SimilarityParamsI; import jalview.api.analysis.ViewBasedAnalysisI; import jalview.bin.Cache; import jalview.commands.CommandI; @@ -41,7 +45,7 @@ import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; import jalview.io.NewickFile; import jalview.jbgui.GTreePanel; -import jalview.schemes.ResidueProperties; +import jalview.util.ImageMaker; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; @@ -70,68 +74,46 @@ import org.jibble.epsgraphics.EpsGraphics2D; */ public class TreePanel extends GTreePanel { - String type; + String treeType; - String pwtype; + ScoreModelI scoreModel; // if tree computed + + String treeTitle; // if tree loaded + + SimilarityParamsI similarityParams; TreeCanvas treeCanvas; - NJTree tree; + TreeModel tree; AlignViewport av; /** * Creates a new TreePanel object. * - * @param av - * DOCUMENT ME! - * @param seqVector - * DOCUMENT ME! + * @param ap * @param type - * DOCUMENT ME! - * @param pwtype - * DOCUMENT ME! - * @param s - * DOCUMENT ME! - * @param e - * DOCUMENT ME! + * @param sm + * @param options */ - public TreePanel(AlignmentPanel ap, String type, String pwtype) + public TreePanel(AlignmentPanel ap, String type, ScoreModelI sm, + SimilarityParamsI options) { super(); - initTreePanel(ap, type, pwtype, null, null); + this.similarityParams = options; + initTreePanel(ap, type, sm, null, null); // We know this tree has distances. JBPNote TODO: prolly should add this as // a userdefined default // showDistances(true); } - /** - * Creates a new TreePanel object. - * - * @param av - * DOCUMENT ME! - * @param seqVector - * DOCUMENT ME! - * @param newtree - * DOCUMENT ME! - * @param type - * DOCUMENT ME! - * @param pwtype - * DOCUMENT ME! - */ - public TreePanel(AlignmentPanel ap, String type, String pwtype, - NewickFile newtree) + public TreePanel(AlignmentPanel alignPanel, NewickFile newtree, + String theTitle, AlignmentView inputData) { super(); - initTreePanel(ap, type, pwtype, newtree, null); - } - - public TreePanel(AlignmentPanel av, String type, String pwtype, - NewickFile newtree, AlignmentView inputData) - { - super(); - initTreePanel(av, type, pwtype, newtree, inputData); + this.treeTitle = theTitle; + initTreePanel(alignPanel, null, null, newtree, inputData); } public AlignmentI getAlignment() @@ -144,13 +126,13 @@ public class TreePanel extends GTreePanel return treeCanvas.av; } - void initTreePanel(AlignmentPanel ap, String type, String pwtype, + void initTreePanel(AlignmentPanel ap, String type, ScoreModelI sm, NewickFile newTree, AlignmentView inputData) { av = ap.av; - this.type = type; - this.pwtype = pwtype; + this.treeType = type; + this.scoreModel = sm; treeCanvas = new TreeCanvas(this, ap, scrollPane); scrollPane.setViewportView(treeCanvas); @@ -180,7 +162,7 @@ public class TreePanel extends GTreePanel .println("new alignment sequences vector value is null"); } - tree.UpdatePlaceHolders((List) evt.getNewValue()); + tree.updatePlaceHolders((List) evt.getNewValue()); treeCanvas.nameHash.clear(); // reset the mapping between canvas // rectangles and leafnodes repaint(); @@ -188,11 +170,7 @@ public class TreePanel extends GTreePanel } }); - TreeLoader tl = new TreeLoader(newTree); - if (inputData != null) - { - tl.odata = inputData; - } + TreeLoader tl = new TreeLoader(newTree, inputData); tl.start(); } @@ -264,19 +242,21 @@ public class TreePanel extends GTreePanel class TreeLoader extends Thread { - NewickFile newtree; + private NewickFile newtree; - jalview.datamodel.AlignmentView odata = null; + private AlignmentView odata = null; - public TreeLoader(NewickFile newtree) + public TreeLoader(NewickFile newickFile, AlignmentView inputData) { - this.newtree = newtree; - if (newtree != null) + this.newtree = newickFile; + this.odata = inputData; + + if (newickFile != null) { // Must be outside run(), as Jalview2XML tries to // update distance/bootstrap visibility at the same time - showBootstrap(newtree.HasBootstrap()); - showDistances(newtree.HasDistances()); + showBootstrap(newickFile.HasBootstrap()); + showDistances(newickFile.HasDistances()); } } @@ -286,60 +266,20 @@ public class TreePanel extends GTreePanel if (newtree != null) { - if (odata == null) - { - tree = new NJTree(av.getAlignment().getSequencesArray(), newtree); - } - else - { - tree = new NJTree(av.getAlignment().getSequencesArray(), odata, - newtree); - } - if (!tree.hasOriginalSequenceData()) + tree = new TreeModel(av.getAlignment().getSequencesArray(), odata, + newtree); + if (tree.getOriginalData() == null) { - allowOriginalSeqData(false); + originalSeqData.setVisible(false); } } else { - int start, end; - SequenceI[] seqs; - boolean selview = av.getSelectionGroup() != null - && av.getSelectionGroup().getSize() > 1; - AlignmentView seqStrings = av.getAlignmentView(selview); - if (!selview) - { - start = 0; - end = av.getAlignment().getWidth(); - seqs = av.getAlignment().getSequencesArray(); - } - else - { - start = av.getSelectionGroup().getStartRes(); - end = av.getSelectionGroup().getEndRes() + 1; - seqs = av.getSelectionGroup().getSequencesInOrder( - av.getAlignment()); - } - ScoreModelI sm = ResidueProperties.getScoreModel(pwtype); - if (sm instanceof ViewBasedAnalysisI) - { - try - { - sm = sm.getClass().newInstance(); - ((ViewBasedAnalysisI) sm) - .configureFromAlignmentView(treeCanvas.ap); - } catch (Exception q) - { - Cache.log.error("Couldn't create a scoremodel instance for " - + sm.getName()); - } - tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end); - } - else - { - tree = new NJTree(seqs, seqStrings, type, pwtype, null, start, - end); - } + ScoreModelI sm = configureScoreModel(); + TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING) ? new NJTree( + av, sm, similarityParams) : new AverageDistanceTree(av, sm, + similarityParams); + tree = new TreeModel(njtree); showDistances(true); } @@ -373,17 +313,12 @@ public class TreePanel extends GTreePanel treeCanvas.setMarkPlaceholders(b); } - private void allowOriginalSeqData(boolean b) - { - originalSeqData.setVisible(b); - } - /** * DOCUMENT ME! * * @return DOCUMENT ME! */ - public NJTree getTree() + public TreeModel getTree() { return tree; } @@ -399,33 +334,14 @@ public class TreePanel extends GTreePanel { CutAndPasteTransfer cap = new CutAndPasteTransfer(); - StringBuffer buffer = new StringBuffer(); + String newTitle = getPanelTitle(); - if (type.equals("AV")) - { - buffer.append("Average distance tree using "); - } - else - { - buffer.append("Neighbour joining tree using "); - } - - if (pwtype.equals("BL")) - { - buffer.append("BLOSUM62"); - } - else - { - buffer.append("PID"); - } - - jalview.io.NewickFile fout = new jalview.io.NewickFile( - tree.getTopNode()); + NewickFile fout = new NewickFile(tree.getTopNode()); try { - cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), - tree.isHasRootDistance())); - Desktop.addInternalFrame(cap, buffer.toString(), 500, 100); + cap.setText(fout.print(tree.hasBootstrap(), tree.hasDistances(), + tree.hasRootDistance())); + Desktop.addInternalFrame(cap, newTitle, 500, 100); } catch (OutOfMemoryError oom) { new OOMWarning("generating newick tree file", oom); @@ -462,8 +378,8 @@ public class TreePanel extends GTreePanel { jalview.io.NewickFile fout = new jalview.io.NewickFile( tree.getTopNode()); - String output = fout.print(tree.isHasBootstrap(), - tree.isHasDistances(), tree.isHasRootDistance()); + String output = fout.print(tree.hasBootstrap(), + tree.hasDistances(), tree.hasRootDistance()); java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter(choice)); out.println(output); @@ -491,7 +407,8 @@ public class TreePanel extends GTreePanel @Override public void originalSeqData_actionPerformed(ActionEvent e) { - if (!tree.hasOriginalSequenceData()) + AlignmentView originalData = tree.getOriginalData(); + if (originalData == null) { jalview.bin.Cache.log .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action."); @@ -513,8 +430,9 @@ public class TreePanel extends GTreePanel } catch (Exception ex) { } - ; - Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(gc); + + Object[] alAndColsel = originalData + .getAlignmentAndColumnSelection(gc); if (alAndColsel != null && alAndColsel[0] != null) { @@ -631,11 +549,11 @@ public class TreePanel extends GTreePanel public CommandI sortAlignmentIn(AlignmentPanel ap) { - AlignmentViewport av = ap.av; - SequenceI[] oldOrder = av.getAlignment().getSequencesArray(); - AlignmentSorter.sortByTree(av.getAlignment(), tree); + AlignmentViewport viewport = ap.av; + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByTree(viewport.getAlignment(), tree); CommandI undo; - undo = new OrderCommand("Tree Sort", oldOrder, av.getAlignment()); + undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment()); ap.paintAlignment(true); return undo; @@ -663,11 +581,11 @@ public class TreePanel extends GTreePanel return treeCanvas.font; } - public void setTreeFont(Font font) + public void setTreeFont(Font f) { if (treeCanvas != null) { - treeCanvas.setFont(font); + treeCanvas.setFont(f); } } @@ -747,24 +665,22 @@ public class TreePanel extends GTreePanel try { - jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] - { "eps" }, new String[] { "Encapsulated Postscript" }, - "Encapsulated Postscript"); - chooser.setFileView(new jalview.io.JalviewFileView()); + JalviewFileChooser chooser = new JalviewFileChooser( + ImageMaker.EPS_EXTENSION, ImageMaker.EPS_EXTENSION); + chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager .getString("label.create_eps_from_tree")); chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); - if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION) + if (value != JalviewFileChooser.APPROVE_OPTION) { return; } - jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser - .getSelectedFile().getParent()); + Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile() + .getParent()); FileOutputStream out = new FileOutputStream(chooser.getSelectedFile()); EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height); @@ -795,10 +711,8 @@ public class TreePanel extends GTreePanel try { - jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] - { "png" }, new String[] { "Portable network graphics" }, - "Portable network graphics"); + JalviewFileChooser chooser = new JalviewFileChooser( + ImageMaker.PNG_EXTENSION, ImageMaker.PNG_DESCRIPTION); chooser.setFileView(new jalview.io.JalviewFileView()); chooser.setDialogTitle(MessageManager @@ -894,12 +808,71 @@ public class TreePanel extends GTreePanel } if (newname != null) { - String oldname = ((SequenceNode) node).getName(); - // TODO : save in the undo object for this modification. + // String oldname = ((SequenceNode) node).getName(); + // TODO : save oldname in the undo object for this modification. ((SequenceNode) node).setName(newname); } } } }); } + + /** + * Formats a localised title for the tree panel, like + *

+ * Neighbour Joining Using BLOSUM62 + *

+ * For a tree loaded from file, just uses the file name + * @return + */ + public String getPanelTitle() + { + if (treeTitle != null) + { + return treeTitle; + } + + /* + * i18n description of Neighbour Joining or Average Distance method + */ + String treecalcnm = MessageManager.getString("label.tree_calc_" + + treeType.toLowerCase()); + + /* + * i18n description (if available) of score model used + */ + String smn = MessageManager.getStringOrReturn("label.score_model_", + scoreModel.getName()); + + /* + * put them together as Using + */ + final String ttl = MessageManager.formatMessage("label.treecalc_title", + treecalcnm, smn); + return ttl; + } + + /** + * If the score model is one that requires to get state data from the current + * view, create and configure a new instance of it + * + * @return + */ + protected ScoreModelI configureScoreModel() + { + if (scoreModel instanceof ViewBasedAnalysisI) + { + try + { + scoreModel = scoreModel.getClass().newInstance(); + ((ViewBasedAnalysisI) scoreModel) + .configureFromAlignmentView(treeCanvas.ap); + } catch (Exception q) + { + Cache.log.error("Couldn't create a scoremodel instance for " + + scoreModel.getName()); + } + } + return scoreModel; + } }